Dear all, On Sat, May 30, 2020 at 03:40:53PM +0100, Eleanor Dodson wrote: > My pennysworth. If you find your maps look better after the > anisotroy correction use it, but it may be helpful to those wo want to mine > your data if you deposit the whole sphere..
Agree (which is what e.g. we provide when using STARANISO via autoPROC [1]). And in the same vein: those depositing isotropically truncated data should consider also providing data to a higher diffraction limit to give a potentially more accurate picture (if there is even a slight indication of anisotropy - which there often is). I find it very helpful even looking at an idealised (and therefore simplified) picture of anisotropy as in http://staraniso.globalphasing.org/anisotropy_about.html We can consider (1) for refinement: (1a) green+red, i.e. spherical (i.e. isotropically) truncated data (1b) green+blue, i.e. anisotropycally truncated data (2) for deposition: (2a) green+red => full sphere, but dropping real observations (blue) (2b) green+blue => all observations, but not providing insignificant/weak data (red) in all directions (2c) a sphere to the "tip" of blue (i.e. anisotropic diffraction limit) => all observations and all insignificant/weak data Cheers Clemens [1] https://www.globalphasing.com/autoproc/ - which gives a mmCIF file with (2a), (2b) and (2c) ready for deposition. > eleanor > > On Sat, 30 May 2020 at 09:36, Robbie Joosten <robbie_joos...@hotmail.com> > wrote: > > > Hi Everyone, > > > > I've been looking at some recent PDB entries that have much lower > > spherical) completeness than reported in the coordinate file. One reason > > for this is that the data were anisotropicly truncated, another reason is > > some mess-up with the deposition of the reflection data. There is a lot of > > discussion about the former practice and I don't want to go in to that, but > > the second one is obviously an error. Now how do I distinguish these cases? > > > > Sometimes, you can look at the reported number of reflections and compare > > that to the deposited reflection file and you will find that something has > > clearly gone wrong. However, the reported number of reflections is not > > entirely reliable because of other issues so I'd rather not use it. If you > > use PDBpeep (e.g. for 6rjy) you can see something is wrong, but that is > > completely visual. Is there a tool in CCP4 that reports both spherical and > > ellipsoidal completeness (on merged reflection data)? That would make it > > easy to distinguish such cases. > > > > Cheers, > > Robbie > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
